I have LOTS to tell you! lol
I have been following your December trip report for along time now but just found your Sept/Oct report today!
First, how long will it take to get from MCO via ME to Pop & check-in? I would say 45 minutes. We stayed at CBR and left MCO on the ME bus at 3:57pm...got to CBR at 4:45pm but our first stop was POP.
CS to eat at each park...I would say at AK Restaurantosaurs, at MK Cosmic Ray's or Pinnochios, DHS ABC Commissary, and Epcot Sunshine Seasons, UK, or Mexico (we liked most places at Epcot, but it just depends on what you like).
Hollywood & Vine...is EXCELLENT! I mean, honestly, the food wasn't that great, but I'm not a fan of any breakfast at Disney. Of all the breakfasts I've had, I loved having the buffet at H&V. It was nice to have a selection & be able to get something else if I didn't like what I had. Also, we all like different things & since DS is only 2 years old (but does eat mostly anything) I was worried about us all enjoying the same meal. However, we all ate at least 4-5 plates of food plus a Mickey waffle & all were full afterwards. As far as the character interaction, it is AMAZING!!! I'm spoiling part of my trip report for you, but all of the characters came around TWICE within about 45-50 minutes! Also, not sure if you know, but the characters there now are Handy Manny, JoJo, and June & Leo (from Little Einsteins). Handy Manny was awesome! I had my DS wear his Handy Manny outfit since he's been his fav character since he was around 6 months old! Manny pointed at his shirt & was really good with my son!

We had a really nice time there. My DH usually doesn't say many good things about restaurants, but he talked about this one all day (he's very very picky about food too). I know it has mixed reviews, but I choose it for Manny...and ended up getting a great meal as well as great character interaction! I hope you have a great experience as well!
I think I saw Toy Story tshirts at Old Navy...but I'm not sure, it might have been Kohls
You might already know this, but I learned the hard way...I would leave around 30-45 minutes anytime you are transferring from your resort to a park. And if you are travelling from resort to park to another resort, leave 45-60 minutes.
When ME comes to pick you up at your resort the day of your departure, they will arrive 3 hours prior. I had forgotten this from last year's trip so I thought I'd mention it, although you probably already know that too!
You will LOVE LOVE LOVE Sept/Oct. I am completely jealous that you are going during that time of the year! My family goes every year in the middle of September & it is AMAZING!!! Seriously, I cannot say enough good things about it. I will have to get some pictures to show you...the parks are pretty much empty!

You won't have to worry about rides at all...most are walk-ons and some have short waits. They rode Kilimanjaro Safaris last year THREE times in a row without waiting! They might have waited like 5 minutes, but there was definitely no need to run & grab fast-passes asap like at other times of the year! They actually could have gone on it 4 times but wanted to go to EE instead...so they rode it 4 times as well.

I was sooo mad when they got back last year because I was so jealous...we went last year during spring break & the parks were a mess! lol
Since our children are around the same age, I wanted to tell you what I did prior to our trip! About 30 days prior to leaving, I showed my son Disney DVDs & read him Disney books

I also got onto
YouTube and searched for the different parades, fireworks, rides, and shows. You can actually find videos on there of the different rides...so lets say you are worried he will be afraid of Haunted Mansion...type it in on YouTube & you can watch the entire ride with him! That is a good determination of what he'll think...although some rides, my son loved watching on the computer screen, but once we got to the park, he was terrified! So, it isn't a 100% accurate, but its a good indication!
I hope my info helps you! Watch for Day 3 on my trip report...thats when we went to Hollywood & Vine for breakfast!!!